sc_MolecularEnergy (3) - Linux Manuals
NAME
sc::MolecularEnergy -
The MolecularEnergy abstract class inherits from the Function class.
SYNOPSIS
#include <energy.h>
Inherits sc::Function.
Inherited by sc::SumMolecularEnergy, sc::TaylorMolecularEnergy, and sc::Wavefunction.
Public Member Functions
MolecularEnergy (const MolecularEnergy &)
MolecularEnergy (const Ref< KeyVal > &)
The KeyVal constructor.
MolecularEnergy (StateIn &)
void save_data_state (StateOut &)
Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them.
void set_checkpoint ()
Set up checkpointing.
void set_checkpoint_file (const char *)
void set_checkpoint_freq (int freq)
bool if_to_checkpoint () const
Check if need to checkpoint.
const char * checkpoint_file () const
int checkpoint_freq () const
MolecularEnergy & operator= (const MolecularEnergy &)
virtual double energy ()
A wrapper around value();.
virtual Ref< Molecule > molecule () const
virtual RefSCDimension moldim () const
void guess_hessian (RefSymmSCMatrix &)
Compute a quick, approximate hessian.
RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
RefSymmSCMatrix hessian ()
If a molecule hessian object is given, it will be used to provide a hessian.
int hessian_implemented () const
void set_x (const RefSCVector &)
Set and retrieve the coordinate values.
RefSCVector get_cartesian_x ()
Return the cartesian coordinates.
RefSCVector get_cartesian_gradient ()
Return the cartesian gradient.
RefSymmSCMatrix get_cartesian_hessian ()
Return the cartesian hessian.
Ref< MolecularCoor > molecularcoor ()
virtual void symmetry_changed ()
Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
Ref< NonlinearTransform > change_coordinates ()
An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system.
void print_natom_3 (const RefSCVector &, const char *t=0, std::ostream &o=ExEnv::out0()) const
Nicely print n x 3 data that are stored in a vector.
void print_natom_3 (double **, const char *t=0, std::ostream &o=ExEnv::out0()) const
void print_natom_3 (double *, const char *t=0, std::ostream &o=ExEnv::out0()) const
virtual void print (std::ostream &=ExEnv::out0()) const
Print information about the object.
Protected Member Functions
void failure (const char *)
virtual void set_energy (double)
This is just a wrapper around set_value().
virtual void set_gradient (RefSCVector &)
These are passed gradients and hessian in cartesian coordinates.
virtual void set_hessian (RefSymmSCMatrix &)
void x_to_molecule ()
void molecule_to_x ()
Protected Attributes
Ref< PointGroup > initial_pg_
int print_molecule_when_changed_
Detailed Description
The MolecularEnergy abstract class inherits from the Function class.
It computes the energy of the molecule as a function of the geometry. The coordinate system used can be either internal or cartesian.
Constructor & Destructor Documentation
sc::MolecularEnergy::MolecularEnergy (const Ref< KeyVal > &)
The KeyVal constructor. .IP "molecule" 1c A Molecule object. There is no default.
- coor
- A MolecularCoor object that describes the coordinates. If this is not given cartesian coordinates will be used. For convenience, two keywords needed by the MolecularCoor object are automatically provided: natom3 and matrixkit.
- value_accuracy
- Sets the accuracy to which values are computed. The default is 1.0e-6 atomic units.
- gradient_accuracy
- Sets the accuracy to which gradients are computed. The default is 1.0e-6 atomic units.
- hessian_accuracy
- Sets the accuracy to which hessians are computed. The default is 1.0e-4 atomic units.
- hessian
- Specifies a MolecularHessian object that is used to compute the hessian. If this MolecularEnergy specialization does not provide a hessian of its own, and a hessian is needed, then this keyword must be specified.
- guess_hessian
- Specifies a MolecularHessian object that is used to compute a guess hessian. Guess hessians are used to improve the rate of convergence of optimizations. If this keyword is not specified, and a MolecularCoor object is given by coor, then the guess hessian is obtained from the MolecularCoor object. If neither this nor coor are given, then Function::guess_hessian is used, which returns a unit matrix.
- print_molecule_when_changed
- If true, then whenever the molecule's coordinates are updated they will be printed. The default is true.
- checkpoint
- If true, then this object will be checkpointed during its evaluation. Not all implementations of MolecularEnergy support checkpointing. The default is false.
- checkpoint_file
- Specifies the name of the file into which this object will be checkpointed. Default is '<inpubasename>.ckpt', where '<inputbasename>' is the name of the input file without '.in'.
- checkpoint_freq
- Specifies how often this object to be checkpointed. Only matters for objects which are computed iteratively. Default is 1.
Member Function Documentation
Ref<NonlinearTransform> sc::MolecularEnergy::change_coordinates () [virtual]
An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. A return value of 0 means the coordinates were not changed. Otherwise, a transform object to the new coordinate system is return. The function object applies the transform to any objects it contains. This will obsolete the function data.
Reimplemented from sc::Function.
RefSymmSCMatrix sc::MolecularEnergy::hessian () [virtual]
If a molecule hessian object is given, it will be used to provide a hessian.
Reimplemented from sc::Function.
void sc::MolecularEnergy::save_data_state (StateOut &) [virtual]
Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. This must be implemented by the derived class if the class has data.
Reimplemented from sc::Function.
Reimplemented in sc::SumMolecularEnergy, sc::TaylorMolecularEnergy, sc::CLKS, sc::HSOSKS, sc::UKS, sc::MBPT2, sc::MP2BasisExtrap, sc::MBPT2_R12, sc::PsiWavefunction, sc::PsiSCF, sc::PsiCCSD, sc::PsiCCSD_T, sc::CLHF, sc::CLSCF, sc::HSOSHF, sc::HSOSSCF, sc::OSSHF, sc::OSSSCF, sc::SCF, sc::TCHF, sc::TCSCF, sc::UHF, sc::UnrestrictedSCF, sc::ExtendedHuckelWfn, sc::OneBodyWavefunction, sc::HCoreWfn, and sc::Wavefunction.
virtual void sc::MolecularEnergy::set_gradient (RefSCVector &) [protected, virtual]
These are passed gradients and hessian in cartesian coordinates. The gradient and hessian in internal coordinates are computed.
Reimplemented from sc::Function.
virtual void sc::MolecularEnergy::symmetry_changed () [virtual]
Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
Reimplemented in sc::MBPT2, sc::CLSCF, sc::HSOSSCF, sc::OSSSCF, sc::SCF, sc::TCSCF, sc::UnrestrictedSCF, sc::OneBodyWavefunction, and sc::Wavefunction.
Author
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